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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools>=62.0", "wheel>=0.37"]
build-backend = "setuptools.build_meta"
[project]
name = "aeon_mecha"
version = "0.1.0"
requires-python = ">=3.11"
description = '''
Code for managing acquired data from Project Aeon experiments. Includes general file IO,
data QC, querying, and analysis modules.
'''
authors = [
{ name = "Jai Bhagat", email = "[email protected]" },
{ name = "Goncalo Lopes", email = "[email protected]" },
{ name = "Thinh Nguyen", email = "[email protected]" },
{ name = "Joseph Burling", email = "[email protected]" },
{ name = "Chang Huan Lo", email = "[email protected]" },
{ name = "Jaerong Ahn", email = "[email protected]" },
]
license = { file = "license.md" }
readme = "readme.md"
dependencies = [
"bottleneck>=1.2.1,<2",
"datajoint-utilities @ git+https://github.com/datajoint-company/datajoint-utilities",
"datajoint>=0.13.7",
"dotmap",
"fastparquet",
"graphviz",
"ipykernel",
"jupyter",
"jupyterlab",
"matplotlib",
"numba>=0.46.0, <1",
"numexpr>=2.6.8, <3",
"numpy>=1.21.0, <2",
"opencv-python",
"pandas>=1.3",
"pillow",
"plotly",
"pyarrow",
"pydotplus",
"pymysql",
"pyyaml",
"scikit-learn",
"scipy",
"seaborn",
"xarray>=0.12.3",
]
[project.optional-dependencies]
dev = [
"bandit",
"black[jupyter]",
"gh",
"ipdb",
"pre-commit",
"pyan3 @ git+https://github.com/Technologicat/pyan.git",
"pydantic",
"pyright",
"pytest",
"pytest-cov",
"sphinx",
"ruff",
"tox",
]
gpu = ["cupy", "dask"]
[project.scripts]
aeon_ingest = "aeon.dj_pipeline.populate.process:cli"
[project.urls]
Homepage = "https://sainsburywellcomecentre.github.io/aeon_docs/"
Repository = "https://github.com/sainsburyWellcomeCentre/aeon_mecha"
Documentation = "https://sainsburywellcomecentre.github.io/aeon_docs/"
DataJoint = "https://docs.datajoint.org/"
[tool.setuptools.packages.find]
include = ["aeon*"]
[tool.black]
line-length = 108
color = false
exclude = '''
/(
\.git
| \.mypy_cache
| \.tox
| \.venv
| _build
| build
| dist
| env
| venv
)/
'''
extend-exclude = "aeon/dj_pipeline/streams.py"
[tool.ruff]
select = [
"E",
"W",
"F",
"I",
"D",
"UP",
"S",
"B",
"A",
"C4",
"ICN",
"PIE",
"PT",
"SIM",
"PL",
]
line-length = 108
ignore = [
"E201",
"E202",
"E203",
"E231",
"E731",
"E702",
"S101",
"PT013",
"PLR0912",
"PLR0913",
"PLR0915",
]
extend-exclude = [
".git",
".github",
".idea",
".vscode",
"aeon/dj_pipeline/streams.py",
]
[tool.ruff.per-file-ignores]
"aeon/dj_pipeline/*" = [
"B006",
"B021",
"D100", # skip adding docstrings for module
"D101", # skip adding docstrings for table class since it is added inside definition
"D102", # skip adding docstrings for make function
"D103", # skip adding docstrings for public functions
"D104", # ignore missing docstring in public package
"D106", # skip adding docstrings for Part tables
"E501",
"F401", # ignore unused import errors
"B905", # ignore unused import errors
"E999",
"S324",
"E722",
"S110",
"F821",
"B904",
"UP038",
"S607",
"S605",
"D205",
"D202",
"F403",
"PLR2004",
"SIM108",
"PLW0127",
"PLR2004",
"I001",
]
[tool.ruff.pydocstyle]
convention = "google"
[tool.pyright]
reportMissingImports = "none"
reportImportCycles = "error"
reportUnusedImport = "error"
reportUnusedClass = "error"
reportUnusedfunction = "error"
reportUnusedVariable = "error"
reportDuplicateImport = "error"
reportWildcardImportFromLibrary = "error"
reportPrivateUsage = "error"
reportCallInDefaultInitializer = "error"
reportUnnecessaryIsInstance = "error"
reportUnnecesaryCast = "error"
reportUnnecesarryComparison = "error"
reportUnnecessaryContains = "error"
reportAssertAlwaysTrue = "error"
reportSelfClsParameterName = "error"
reportUnusedExpression = "error"
reportMatchNotExhaustive = "error"
reportShadowedImports = "error"
# *Note*: we may want to set all 'ReportOptional*' rules to "none", but leaving 'em default for now
venvPath = "."
venv = ".venv"
exclude = ["aeon/dj_pipeline/*"]
[tool.pytest.ini_options]
markers = ["api"]